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Text Mining for Search Strategy Development

PubVenn

PubVenn allows you to explore PubMed visually by generating Venn diagrams. You can enter any multi-term search to generate a Venn diagram that allows you to view the size of the citation set for each term as well as how those sets interact.

Availability Free online
Data Source PubMed
Tool Type Visualisation tool
Features Provides example PubMed search strategy and links to relevant publications.
Selecting the 'Expanded subjects' checkbox will include other relevant terms from PubMed.
Import Formats Free text
Export Formats Save as .png
Known Limitations PubMed data only
URL

https://pubvenn.appspot.com/

Also try Search Workbench https://searchworkbench.info/

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Free Text input: Depressive Disorder AND Serotonin Uptake AND Hypericum
Search translation: (depressive disorder[MeSH Terms] OR (depressive[All Fields] AND disorder[All Fields]) OR depressive disorder[All Fields]) AND (serotonin uptake inhibitors[Pharmacological Action] OR serotonin uptake inhibitors[MeSH Terms] OR (serotonin[All Fields] AND uptake[All Fields] AND inhibitors[All Fields]) OR serotonin uptake inhibitors[All Fields]) AND (hypericum[MeSH Terms] OR hypericum[All Fields]): 57

PubMed PubReMiner

Enter a free text search into the PubReMiner tool and it will query PubMed for relevant results.
The tool analyses these results and provides tables that rank the frequency of words in the title and abstract of the articles and also relevant MeSH headings. Other ranked tables include journals in which your query is published the most and authors which are most active in related fields.

Availability Free online
Data Source PubMed
Tool Type Text frequency
Features Self selection of elements to display in the results. Direct connection to PubMed.
Import Formats Free text
Export Formats Save results as a .txt file
Known Limitations Limited to PubMed
URL http://hgserver2.amc.nl/cgi-bin/miner/miner2.cgi
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Coremine

Coremine Medical is a product of the PubGene Company designed to be used by anyone seeking information on health, medicine and biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to "drill down" to specific details. Search results are presented in a dashboard format comprised of panels containing various categories of information ranging from introductory sources to the latest scientific articles. Coremine presents search results as a graphic network that describes relationships discovered through text-mining.

Availability
Data Source PubMed
Tool Type Visualisation, clustering, text frequency, relationship networks
Features File upload, Hyperbrowser, search history, alerts.
Import Formats Free text, tab delimited file can be uploaded
Export Formats None
Known Limitations
URL
Instructions
https://www.coremine.com/medical/
https://www.coremine.com/medical/help.html
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MeSH on Demand

The MeSH on Demand tool uses the NLM Medical Text Indexer to identifiy MeSH vocabulary in submitted text (paste up to five pages). The results are displayed in a list as well as highlighted in the pasted text (also defines term frequency within the text). Links to similar PubMed related citations are included.
Availability Free online
Data Source PubMed
Tool Type Text analyser
Features Suggests MeSH vocabulary found in similar, related citations as well as the submitted text.
Import Formats Free text (paste)
Export Formats Text file
Known Limitations Non English text needs to be translated first.
URL https://meshb.nlm.nih.gov/MeSHonDemand
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Yale MeSH Analyser

Availability Free online
Data Source PubMed
Tool Type Comparison
Features Easy to view comparison of article indexing
Import Formats Free text (type or paste)
Export Formats Excel, HTML table
Known Limitations Query with PubMed IDs only - maximum 20
URL http://mesh.med.yale.edu
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HelioBLAST

HelioBLAST is a free service provided by HelioText. The HelioBLAST text similarity engine finds text records that are similar to the submitted query. Your query is searched against the citations (abstract and titles) in Medline/PubMed and the top matching articles are returned in the results

Availability Free online
Data Source PubMed
Tool Type Word analysis
Features 'Implicit keywords' - additional word frequency analysis tool
Import Formats Free text - copy and paste
Export Formats No export function but links to article records in PubMed
Known Limitations Limit of 1000 words
URL https://helioblast.heliotext.com/
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Carrot2

Carrot2 is an Open Source Results Clustering Engine that can automatically organise search results into topics. Carrot2 can query PubMed and allows boolean searching.
Availability Free online, download
Data Source PubMed
Tool Type Clustering
Features Simple online interface
Import Formats Free text
Export Formats View on screen
Known Limitations No export options
URL https://search.carrot2.org/#/search/web
Images
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